Signatures within the esophageal microbiome are associated with host genetics, age, and disease

Study information

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study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

30558669

DOI Digital object identifier for electronic documents.

https://doi.org/10.1186/s40168-018-0611-4

URI

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4

Authors

Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR, Kaakoush NO

Journal

Microbiome

Year

2018

Keywords:

Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms

BACKGROUND: The esophageal microbiome has been proposed to be involved in a range of diseases including the esophageal adenocarcinoma cascade; however, little is currently known about its function and relationship to the host. Here, the esophageal microbiomes of 106 prospectively recruited patients were assessed using 16S rRNA and 18S rRNA amplicon sequencing as well as shotgun sequencing, and associations with age, gender, proton pump inhibitor use, host genetics, and disease were tested. RESULTS: The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. While age was found to be a significant factor driving microbiome composition, bacterial signatures and functions such as enrichment with Gram-negative oral-associated bacteria and microbial lactic acid production were associated with the early stages of the esophageal adenocarcinoma cascade. Non-bacterial microbes such as archaea, Candida spp., and bacteriophages were also identified in low abundance in the esophageal microbiome. Specific host SNPs in NOTCH2, STEAP2-AS1, and NREP were associated with the composition of the esophageal microbiome in our cohort. CONCLUSIONS: This study provides the most comprehensive assessment of the esophageal microbiome to date and identifies novel signatures and host markers that can be investigated further in the context of esophageal adenocarcinoma development.

Experiment 1

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Curated date: 2024/05/11

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Subjects

Location of subjects

Australia

Host species Species from which microbiome was sampled. Contact us to have more species added.

Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

Esophagus Gullet,Oesophagus,Esophagus,esophagus

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Microbiome measurement Microbiome measurement,microbiome measurement

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Cluster 1

Group 1 name Corresponds to the case (exposed) group for case-control studies

Cluster 2

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

The esophageal microbiome was found to cluster into functionally distinct community types (esotypes)

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

2 months

Lab analysis

Sequencing type

16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance

Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).

relative abundances

Statistical test

LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)

0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

No

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

decreased

Simpson Estimator of species richness and species evenness: more weight on species evenness

decreased

Richness Number of species

decreased

Signature 1

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Curated date: 2024/05/16

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Source: Additional file 1, page 6

Description: The esophageal microbiome clusters into different community types

Abundance in Group 1: increased abundance in Cluster 2

NCBI	Quality Control	Links
Bacilli
Lactobacillales
Porphyromonas
Prevotella
Streptococcaceae
Streptococcus
unclassified Bacillales

Revision editor(s): Fiddyhamma

Signature 2

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Source: Additional file 1, page 6

Description: Description: The esophageal microbiome clusters into different community types

Abundance in Group 1: decreased abundance in Cluster 2

NCBI	Quality Control	Links
Prevotella

Revision editor(s): Fiddyhamma

Experiment 2

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies

Cluster 3

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness

unchanged

Richness Number of species

unchanged

Signature 1

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Curated date: 2024/05/16

Curator: Fiddyhamma

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Source: Additional file 1, page 6

Description: The esophageal microbiome clusters into different community types

Abundance in Group 1: increased abundance in Cluster 3

NCBI	Quality Control	Links
Actinomyces
Actinomycetaceae
Actinomycetales
Actinomycetota
Atopobium
Bacteroidales
Bacteroidia
Coriobacteriaceae
Coriobacteriales
Granulicatella
Kingella
Lachnoanaerobaculum
Lachnospiraceae
Megasphaera
Mogibacterium
Negativicutes
Prevotella
Prevotellaceae
Selenomonadales
Streptococcus
Veillonella
Veillonellaceae
unclassified Carnobacteriaceae
unclassified Lachnospiraceae
unclassified Veillonellaceae

Revision editor(s): Fiddyhamma

Signature 2

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Curated date: 2024/05/25

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Source: Additional file 1, page 6

Description: The esophageal microbiome clusters into different community types

Abundance in Group 1: decreased abundance in Cluster 3

NCBI	Quality Control	Links
Prevotella

Revision editor(s): Fiddyhamma

Experiment 3

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Curated date: 2024/05/11

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Cluster 2

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness

unchanged

Richness Number of species

unchanged

Signature 1

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/05/16

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

Source: Additional file 1, page 6

Description: The esophageal microbiome clusters into different community types   

Abundance in Group 1: increased abundance in Cluster 3

NCBI	Quality Control	Links
Actinomyces
Actinomycetaceae
Actinomycetales
Actinomycetota
Atopobium
Bacteroidales
Bacteroidia
Coriobacteriaceae
Coriobacteriales
Granulicatella
Kingella
Lachnoanaerobaculum
Lachnospiraceae
Megasphaera
Mogibacterium
Negativicutes
Prevotella
Prevotellaceae
Selenomonadales
Veillonella
Veillonellaceae
unclassified Carnobacteriaceae
unclassified Lachnospiraceae
unclassified Prevotellaceae
unclassified Veillonellaceae

Revision editor(s): Fiddyhamma

Signature 2

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/05/16

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

Source: Additional file 1, page 6

Description: The esophageal microbiome clusters into different community types

Abundance in Group 1: decreased abundance in Cluster 3

NCBI	Quality Control	Links
Bacilli
Lactobacillales
Porphyromonas
Prevotella
Streptococcaceae
Streptococcus
unclassified Bacillales

Revision editor(s): Fiddyhamma

Experiment 4

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Curated date: 2024/05/25

Curator: Fiddyhamma

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Cluster 1

Group 1 name Corresponds to the case (exposed) group for case-control studies

Cluster 2

Lab analysis

Sequencing type

WMS

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

decreased

Simpson Estimator of species richness and species evenness: more weight on species evenness

decreased

Richness Number of species

decreased

Signature 1

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/05/25

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

Source: Additional file 1, page 7

Description: The esophageal microbiome clusters into different community types   

Abundance in Group 1: increased abundance in Cluster 2

NCBI	Quality Control	Links
Bacilli

Revision editor(s): Fiddyhamma

Signature 2

EditHistoryDelete

Mark reviewed

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Needs review

Curated date: 2024/05/29

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

Source: Additional file 1, page 7

Description: The esophageal microbiome clusters into different community types

Abundance in Group 1: decreased abundance in Cluster 2

NCBI	Quality Control	Links
Actinomycetales
Actinomycetota
Capnocytophaga
Flavobacteriaceae
Flavobacteriales
Flavobacteriia
Gammaproteobacteria
Haemophilus
Haemophilus parainfluenzae
Pasteurellaceae
Pasteurellales
Pseudomonadota
Rothia
Rothia mucilaginosa
unclassified Granulicatella
Micrococcaceae

Revision editor(s): Fiddyhamma

Experiment 5

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Curated date: 2024/05/25

Curator: Fiddyhamma

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies

Cluster 3

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness

unchanged

Richness Number of species

unchanged

Signature 1

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/05/29

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

Source: Additional file 1, page 7

Description: The esophageal microbiome clusters into different community types

Abundance in Group 1: increased abundance in Cluster 3

NCBI	Quality Control	Links
Bacteroidia
Bacteroidales
Negativicutes
Selenomonadales
Veillonellaceae
Veillonella
unclassified Veillonella
Prevotella histicola
Prevotella veroralis
Prevotella pallens

Revision editor(s): Fiddyhamma

Signature 2

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Curated date: 2024/05/29

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

Source: Additional file 1, page 7

Description: The esophageal microbiome clusters into different community types   

Abundance in Group 1: decreased abundance in Cluster 3

NCBI	Quality Control	Links
Actinomycetales
Actinomycetota
Capnocytophaga
Flavobacteriaceae
Flavobacteriales
Flavobacteriia
Gammaproteobacteria
Haemophilus
Haemophilus parainfluenzae
Micrococcaceae
Pasteurellaceae
Pasteurellales
Pseudomonadota
Rothia mucilaginosa
unclassified Granulicatella
Rothia

Revision editor(s): Fiddyhamma

Experiment 6

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Needs review

Curated date: 2024/05/25

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Cluster 2

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness

unchanged

Richness Number of species

unchanged

Signature 1

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/05/29

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

Source: Additional file 1, page 7

Description: The esophageal microbiome clusters into different community types

Abundance in Group 1: increased abundance in Cluster 3

NCBI	Quality Control	Links
Prevotella pallens
Prevotella veroralis
Prevotella histicola
Veillonella
unclassified Veillonella
Veillonellaceae
Selenomonadales
Negativicutes
Bacteroidales
Bacteroidia

Revision editor(s): Fiddyhamma

Signature 2

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/05/29

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

Source: Additional file 1, page 7

Description: The esophageal microbiome clusters into different community types

Abundance in Group 1: decreased abundance in Cluster 3

NCBI	Quality Control	Links
Bacilli

Revision editor(s): Fiddyhamma

Experiment 7

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Needs review

Curated date: 2024/06/01

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Not specified

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Normal

Group 1 name Corresponds to the case (exposed) group for case-control studies

GERD

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Differences across disease subgroups using LEfSe analysis.

Group 0 sample size Number of subjects in the control (unexposed) group

59

Group 1 sample size Number of subjects in the case (exposed) group

29

Lab analysis

Statistical Analysis

Experiment 8

EditHistoryDeleteDuplicate this ExperimentAdd a new Signature

incomplete

Curated date: 2024/06/01

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Microbiome measurement Microbiome measurement,microbiome measurement

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Cluster 2

Group 1 name Corresponds to the case (exposed) group for case-control studies

Cluster 3

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

The esophageal microbiome was found to cluster into functionally distinct community types (esotypes)

Group 0 sample size Number of subjects in the control (unexposed) group

Not specified

Group 1 sample size Number of subjects in the case (exposed) group

Not specified

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).

Not specified

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness

unchanged

Richness Number of species

unchanged